function [metaboliteList, stoichCoeffList, revFlag] = parseRxnFormula(formula)
% Parses reaction formula into a list of metabolites and a
% list of `S` coefficients
%
% USAGE:
%
%    [metaboliteList, stoichCoeffList, revFlag] = parseRxnFormula(formula)
%
% INPUT:
%    formula:           Reaction formula, may contain symbols '+', '->', '<=>' in
%                       addition to stoichiometric coefficients and metabolite names
%                       examples:
%                       '0.01 cdpdag-SC[m] + 0.01 pg-SC[m]  -> 0.01 clpn-SC[m] + cmp[m] + h[m]' (irreversible reaction)
%                       'cit[c] + icit[x]  <=> cit[x] + icit[c] ' (reversible reaction)
%                       If no stoichiometric coefficient is provided, it is assumed
%                       to be = 1.
%                       Reaction formula should be a string, not a cell array
%
% OUTPUTS:
%    metaboliteList:     Cell array with metabolite names
%    stoichCoeffList:    List of `S` coefficients
%    revFlag:            Indicates whether the reaction is reversible (true) or not (false)
%
% EXAMPLE:
%
%    formula = '0.01 cdpdag-SC[m] + 0.01 pg-SC[m]  -> 0.01 clpn-SC[m] + cmp[m] + h[m]'
%
%    [metaboliteList, stoichCoeffList, revFlag] = parseRxnFormula(formula)
%
%    %metaboliteList = 'cdpdag-SC[m]'    'pg-SC[m]'    'clpn-SC[m]'    'cmp[m]'    'h[m]'
%    %stoichCoeffList = -0.01 -0.01 0.01 1 1
%    %revFlag = false
%
% .. Authors:
%       - Markus Herrgard 6/1/07
%       - Richard Que 1/25/10 Modified to handle '-->' and '<==>' as arrows
%         as well as reactionsformatted as '[compartment] : A --> C'.
%       - IT May 2012 Modified to handle '=>'

tokens = splitString(formula);

stoichCoeffList = [];
metaboliteList = {};
revFlag = true;

% Marks the start of a new stoichiometry + metabolite block
newMetFlag = true;
% Designates products vs reactants
productFlag = false;
compartment = '';
for i = 1:length(tokens)
    t = tokens{i};
    if strcmp(t(1),'[')
        %set compartment
        compartment = t;
    elseif strcmp(t,':')
        %Do nothing
    elseif strcmp(t,'+')
        % Do nothing
        newMetFlag = true;
    elseif strcmp(t,'->') || strcmp(t,'-->') || strcmp(t,'=>')
        % Irreversible
        revFlag = false;
        productFlag = true;
        newMetFlag = true;
    elseif strcmp(t,'<=>') || strcmp(t,'<==>')
        % Reversible
        revFlag = true;
        productFlag = true;
        newMetFlag = true;
    else
        sCoeff = str2double(t);
        if (~isnan(sCoeff))
            % Stoich coefficient
            if ~productFlag
                sCoeff = -sCoeff;
            end
            stoichCoeffList(end+1) = sCoeff;
            newMetFlag = false;
        else
            % Metabolite name
            metaboliteList{end+1} = strcat(t,compartment);
            if newMetFlag
                if ~productFlag
                    stoichCoeffList(end+1) = -1;
                else
                    stoichCoeffList(end+1) = 1;
                end
                newMetFlag = true;
            end
        end
    end
end
